| Variant ID: vg1222876583 (JBrowse) | Variation Type: SNP |
| Chromosome: chr12 | Position: 22876583 |
| Reference Allele: A | Alternative Allele: T |
| Primary Allele: A | Secondary Allele: T |
Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.92, T: 0.08, others allele: 0.00, population size: 76. )
TGCTTGACTGCCTCGAGGAGTCACTGCTCGCACAAAAAGCTATCAAGGAAGTGGGTGACGGTTGGCACTACTGGAGCTAGCCTATGTGTTGATTTTTTTT[A/T]
AAAAAAAACAATTTCTACTCTACAAGTGATAGTACTGCTCAAACATATGGAGTATATCACTGAGGTCCATTTCAATATTGCTGGTTCCCAAACCGACAGT
ACTGTCGGTTTGGGAACCAGCAATATTGAAATGGACCTCAGTGATATACTCCATATGTTTGAGCAGTACTATCACTTGTAGAGTAGAAATTGTTTTTTTT[T/A]
AAAAAAAATCAACACATAGGCTAGCTCCAGTAGTGCCAACCGTCACCCACTTCCTTGATAGCTTTTTGTGCGAGCAGTGACTCCTCGAGGCAGTCAAGCA
| Populations | Population Size | Frequency of A(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 53.30% | 40.40% | 3.47% | 2.88% | NA |
| All Indica | 2759 | 28.20% | 63.70% | 3.52% | 4.53% | NA |
| All Japonica | 1512 | 88.60% | 7.20% | 4.10% | 0.13% | NA |
| Aus | 269 | 89.20% | 7.10% | 0.74% | 2.97% | NA |
| Indica I | 595 | 54.10% | 38.80% | 7.06% | 0.00% | NA |
| Indica II | 465 | 27.30% | 51.80% | 1.94% | 18.92% | NA |
| Indica III | 913 | 17.60% | 80.30% | 1.53% | 0.55% | NA |
| Indica Intermediate | 786 | 21.50% | 70.40% | 4.07% | 4.07% | NA |
| Temperate Japonica | 767 | 84.50% | 8.50% | 6.78% | 0.26% | NA |
| Tropical Japonica | 504 | 96.80% | 2.20% | 0.99% | 0.00% | NA |
| Japonica Intermediate | 241 | 84.20% | 13.70% | 2.07% | 0.00% | NA |
| VI/Aromatic | 96 | 90.60% | 8.30% | 1.04% | 0.00% | NA |
| Intermediate | 90 | 80.00% | 16.70% | 2.22% | 1.11% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg1222876583 | A -> DEL | N | N | silent_mutation | Average:48.628; most accessible tissue: Zhenshan97 young leaf, score: 61.964 | N | N | N | N |
| vg1222876583 | A -> T | LOC_Os12g37280.1 | intron_variant ; MODIFIER | silent_mutation | Average:48.628; most accessible tissue: Zhenshan97 young leaf, score: 61.964 | N | N | N | N |
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg1222876583 | NA | 3.04E-06 | mr1030 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1222876583 | NA | 9.08E-06 | mr1069 | Jap_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1222876583 | 5.71E-06 | 8.09E-07 | mr1962 | Jap_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg1222876583 | NA | 1.51E-10 | mr1565_2 | All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |